iASeq: integrative analysis of allele-specificity of protein-DNA interactions in multiple ChIP-seq datasets

BMC Genomics

Table 1 Comparison of iASeq and AlleleSeq

Gold standard	ChrX			All Caltech ASE exonic SNPs			Autosomal Caltech ASE exonic SNPs
TF	T_d	AlleleSeq	iASeq	T_d	AlleleSeq	iASeq	T_d	AlleleSeq	iASeq
YaleCFOS	41	3	4	9	5	3	9	5	3
YaleMYC	122	9	22	39	5	10	38	5	10
YaleJUND	289	13	31	24	4	8	23	4	7
YaleMAX	105	3	18	18	3	1	18	3	2
YalePolIII	25	2	2	0	0	0	0	0	0

Column 1: TF name. Column 2: T_dis the number of AlleleSeq reported ASB SNPs. Columns 3-4: the number of non-pseudoautosomal region X chromosome SNPs among the top T_dallele-specific SNPs reported by AlleleSeq and iASeq. Column 5: T_dis the number of AlleleSeq reported ASB SNPs that had an exonic SNP within their 10kb neighborhood. Columns 6-7 show among the top T_dallele-specific SNPs reported by AlleleSeq and iASeq, how many SNPs had ≥1 exonic ASE SNP in their 10kb neighborhood according to the Caltech RNA-seq experiment. Column 8: T_dis the number of AlleleSeq reported autosomal ASB SNPs that had an exonic SNP within their 10kb neighborhood. Columns 9-10 show among the top T_dautosomal allele-specific SNPs reported by AlleleSeq and iASeq, how many SNPs had ≥1 exonic ASE SNP in their 10kb neighborhood according to the Caltech RNA-seq experiment. Additional file 7: Table S3 contains similar results using Yale RNA-seq exonic ASE SNPs as gold standard.

ISSN: 1471-2164